:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'stringmlst' .. highlight: bash stringmlst ========== .. conda:recipe:: stringmlst :replaces_section_title: :noindex: Fast k\-mer based tool for multi locus sequence typing \(MLST\) directly from genome sequencing reads :homepage: https://github.com/jordanlab/stringMLST :license: CC BY-NC-SA 4.0 :recipe: /`stringmlst `_/`meta.yaml `_ .. conda:package:: stringmlst |downloads_stringmlst| |docker_stringmlst| :versions: .. raw:: html
0.6.3-00.6.2-10.6.2-00.6.1-00.5.1-00.5.1a-10.5.1a-00.4.2-00.4.1-0 ``0.6.3-0``,  ``0.6.2-1``,  ``0.6.2-0``,  ``0.6.1-0``,  ``0.5.1-0``,  ``0.5.1a-1``,  ``0.5.1a-0``,  ``0.4.2-0``,  ``0.4.1-0``,  ``0.4-0``,  ``0.3.7-0``,  ``0.3.6.1-0`` .. raw:: html
:depends bedtools: :depends bwa: :depends lxml: :depends pyfaidx: :depends python: ``>=3`` :depends samtools: ``>=1.0`` :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`set-up-channels`). While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see `here `_ for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others. Given that you already have a conda environment in which you want to have this package, install with:: mamba install stringmlst and update with:: mamba update stringmlst To create a new environment, run:: mamba create --name myenvname stringmlst with ``myenvname`` being a reasonable name for the environment (see e.g. the `mamba docs `_ for details and further options). Alternatively, use the docker container:: docker pull quay.io/biocontainers/stringmlst: (see `stringmlst/tags`_ for valid values for ````) .. |downloads_stringmlst| image:: https://img.shields.io/conda/dn/bioconda/stringmlst.svg?style=flat :target: https://anaconda.org/bioconda/stringmlst :alt: (downloads) .. |docker_stringmlst| image:: https://quay.io/repository/biocontainers/stringmlst/status :target: https://quay.io/repository/biocontainers/stringmlst .. _`stringmlst/tags`: https://quay.io/repository/biocontainers/stringmlst?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/stringmlst/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/stringmlst/README.html